Cited by 343Genomics and Chromatin DynamicsFungal and yeast genetics researchGene Regulatory Network Analysis

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Integrating regulatory motif discovery and genome-wide expression analysis

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Conlon, Erin M., Liu, X. Shirley, Lieb, Jason D., Liu, Jun S.·2003·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.0630591100PMC PMC152294

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Abstract

We propose motif regressor for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. motif regressor is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions. When applied to Saccharomyces cerevisiae , motif regressor identified the ROX1 and YAP1 motifs from Rox1p and Yap1p overexpression experiments, respectively; predicted that Gcn4p may have increased activity in YAP1 deletion mutants; reported a group of motifs (including GCN4, PHO4, MET4, STRE, USR1, RAP1, M3A, and M3B) that may mediate the transcriptional response to amino acid starvation; and found all of the known cell-cycle regulation motifs from 18 expression microarrays over two cell cycles.

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Authors: Conlon, E. M., Liu, X. S., Lieb, J. D., & Liu, J. S.
Affiliations: University of North Carolina at Chapel Hill (US)
Corresponding author: Liu, X. Shirley
ORCID: Conlon, Erin M.
Liu, X. Shirley
Liu, Jun S.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2003-03-07
Volume: 100
Issue: 6
Pages: 3339-3344
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.0630591100
PMC: PMC152294
OpenAlex: W2096139934
Cited by: 343
References: 32
Citations by year: 2026: 1 · 2025: 2 · 2023: 6 · 2022: 2 · 2021: 2 · 2020: 7 · 2019: 8 · 2018: 5 · 2017: 2 · 2016: 11 · 2015: 9 · 2014: 6 · 2013: 11 · 2012: 21
FWCI: 12.32
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
UNC Libraries
Funders: National Science Foundation (0204674)
Helen Hay Whitney Foundation
National Institutes of Health
National Human Genome Research Institute (R01HG002518, R01-HG02518-01)
U.S. National Library of Medicine (1F37 LM 07626-01, F37LM007626)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords: regulatory motif discovery, upstream promoter sequences, gene expression changes, transcription factor binding sites, Saccharomyces cerevisiae, Gcn4p, cell cycle regulation, transcriptional regulation
MeSH terms: Algorithms, Base Sequence, Cell Cycle, DNA, Fungal, Genes, Fungal, Genes, Regulator, Saccharomyces cerevisiae, Linear Models, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Genomics

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Integrating regulatory motif discovery and genome-wide expression analysis

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